Research Topics
| D J LipmanSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 virusesEdward C Holmes
Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
PLoS Biol 3:e300. 2005....- Splign: algorithms for computing spliced alignments with identification of paralogsYuri Kapustin
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
Biol Direct 3:20. 2008..Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms... - Differences in evolutionary pressure acting within highly conserved ortholog groupsTeresa M Przytycka
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 8:208. 2008..g. Proteobacteria or Firmicutes)... - The relationship of protein conservation and sequence lengthDavid J Lipman
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
BMC Evol Biol 2:20. 2002..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints... - Making (anti)sense of non-coding sequence conservationD J Lipman
National Center for Biotechnology Information, National Library of Medicine, NIH, Building 38A 8N803, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 25:3580-3. 1997..The formation of such duplexes may be essential for recognition by post-transcriptional regulatory systems. The conservation may then be explained by selection against the dominant negative effect of allelic divergence... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D46-51. 2010..Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 36:D13-21. 2008..Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - GenBankD A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 25:1-6. 1997..All of NCBI's services are offered through the World Wide Web. In addition, there are specialized server/client versions as well as FTP and e-mail server access... - GenBankD A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 26:1-7. 1998..In addition to FTP, e-mail and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services of interest to biologists... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 31:23-7. 2003..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov... - GenBank: updateDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 32:D23-6. 2004..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov... - GenBankD A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 28:15-8. 2000..NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov.. - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 37:D5-15. 2009..Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 35:D21-5. 2007..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov)... - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D5-16. 2010..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 36:D25-30. 2008..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov... - The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent agesYuri I Wolf
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Proc Natl Acad Sci U S A 106:7273-80. 2009..Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Nucleic Acids Res 37:D26-31. 2009..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 35:D5-12. 2007..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 34:D173-80. 2006..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov... - Database resources of the National Center for Biotechnology InformationEric W Sayers
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 39:D38-51. 2011..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 30:17-20. 2002..NCBI also offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov... - CDART: protein homology by domain architectureLewis Y Geer
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
Genome Res 12:1619-23. 2002..Searches can be further refined by taxonomy and by selecting domains of interest. CDART is available at http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi... - Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRsSvetlana A Shabalina
National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
Nucleic Acids Res 31:5433-9. 2003..Our results provide evidence on the importance of moderately conserved regions in 3'UTRs and suggest that regulatory functions of 3'UTRs might utilize gene-specific information in these regions... - Database resources of the National Center for Biotechnology InformationDavid L Wheeler
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 33:D39-45. 2005..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov... - GenBankDennis A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 34:D16-20. 2006..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov... - Extracting protein alignment models from the sequence databaseA F Neuwald
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 25:1665-77. 1997..Moreover, this method automatically generates models of these ancient conserved regions for rapid and sensitive screening of sequences... - Gapped BLAST and PSI-BLAST: a new generation of protein database search programsS F Altschul
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 25:3389-402. 1997..PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily... - Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genesYuri I Wolf
National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
Genome Biol Evol 2:190-9. 2010..Together the intrinsic constraints and translation rate account for approximately 50% of the variance of the ERs. The contribution of constraints is estimated to be 3- to 5-fold greater than the contribution of translation rate... - Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signalsSvetlana A Shabalina
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 32:1774-82. 2004.... - GenBankD A Benson
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 27:12-7. 1999..The GenBank database and related resources are freely accessible via the URL: http://www.ncbi.nlm.nih.gov.. - GenBankDennis A Benson
Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 33:D34-8. 2005..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov... - Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usageYang Huang
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 37:6799-810. 2009..Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences... - Stochastic processes are key determinants of short-term evolution in influenza a virusMartha I Nelson
Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
PLoS Pathog 2:e125. 2006..Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis... 
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolutionElodie Ghedin
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, Maryland 20850, USA
Nature 437:1162-6. 2005..All data from this project are being deposited, without delay, in public archives...- Comment on "Large-scale sequence analysis of avian influenza isolates"Edward C Holmes
Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
Science 313:1573; author reply 1573. 2006..However, we show that this observation is likely to be an artifact related to the location of PB1-F2 in the +1 reading frame of the PB1 gene...